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Virus Genes

, Volume 55, Issue 1, pp 51–59 | Cite as

VARV B22R homologue as phylogenetic marker gene for Capripoxvirus classification and divergence time dating

  • Bina MishraEmail author
  • Piyali Mondal
  • C. L. Patel
  • Insha Zafir
  • Rachna Gangwar
  • Neha Singh
  • Joyshikh Sonowal
  • Deepanker Bisht
  • Amit Ranjan Sahu
  • Mumtaz Baig
  • Basavaraj Sajjanar
  • R. K. Singh
  • Ravi Kumar Gandham
Article
  • 56 Downloads

Abstract

Sheeppox disease is associated with significant losses in sheep production world over. The sheep pox virus, the goatpox virus, and the lumpy skin disease virus cannot be distinguished by conventional serological tests. Identification of these pathogens needs molecular methods. In this study, seven genes viz. EEV maturation protein—F12L, Virion protein—D3R, RNA polymerase subunit—A5R, Virion core protein—A10L, EEV glycoprotein—A33R, VARV B22R homologue, and Kelch like protein—A55R that cover the start, middle, and end of the genome were selected. These genes were amplified from Roumanian-Fanar vaccine strain and Jaipur virulent strain, cloned, and sequenced. On analysis with the available database sequences, VARV B22R homologue was identified as a marker for phylogenetic reconstruction for classifying the sheeppox viruses of the ungulates. Further, divergence time dating with VARV B22R gene accurately predicted the sheeppox disease outbreak involving Jaipur virulent strain.

Keywords

Sheeppox virus Goatpox virus Lumpy skin disease virus Phylogeny Capripoxvirus Divergence time dating 

Notes

Acknowledgements

This study was supported by ICAR-Indian Veterinary Research Institute and BioCARE, Department of Biotechnology, Government of India.

Author Contributions

BM, GRK and RKS designed the study. BM, PM, CLP, IZ, RG, NS, DB and JS performed the laboratory work. IZ, ARS, MB, BS and GRK performed phylogenetic analysis and wrote the manuscript.

Compliance with ethical standards

Conflict of interest

All authors in this paper declare they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Research involving human participants

No human subjects were involved in this study.

Supplementary material

11262_2018_1613_MOESM1_ESM.pdf (243 kb)
Multiple sequence alignment of EEV maturation protein gene sequences (PDF 242 KB)
11262_2018_1613_MOESM2_ESM.pdf (186 kb)
Multiple sequence alignment of EEV maturation protein amino acid sequences (PDF 185 KB)
11262_2018_1613_MOESM3_ESM.pdf (248 kb)
Multiple sequence alignment of Virion protein gene-D3R gene sequences (PDF 248 KB)
11262_2018_1613_MOESM4_ESM.pdf (184 kb)
Multiple sequence alignment of Virion protein gene-D3R amino acid sequences (PDF 184 KB)
11262_2018_1613_MOESM5_ESM.pdf (193 kb)
Multiple sequence alignment of RNA polymerase subunit -A5R gene sequences (PDF 192 KB)
11262_2018_1613_MOESM6_ESM.pdf (164 kb)
Multiple sequence alignment of RNA polymerase subunit -A5R amino acid sequences (PDF 163 KB)
11262_2018_1613_MOESM7_ESM.pdf (274 kb)
Multiple sequence alignment of Virion core protein -A10L gene sequences (PDF 274 KB)
11262_2018_1613_MOESM8_ESM.pdf (185 kb)
Multiple sequence alignment of Virion core protein -A10L amino acid sequences (PDF 184 KB)
11262_2018_1613_MOESM9_ESM.pdf (205 kb)
Multiple sequence alignment of EEV glycoprotein -A33R gene sequences (PDF 204 KB)
11262_2018_1613_MOESM10_ESM.pdf (168 kb)
Multiple sequence alignment of EEV glycoprotein -A33R gene amino acid sequences (PDF 167 KB)
11262_2018_1613_MOESM11_ESM.pdf (256 kb)
Multiple sequence alignment of VARVB22R homologue gene sequences (PDF 255 KB)
11262_2018_1613_MOESM12_ESM.pdf (188 kb)
Multiple sequence alignment of VARVB22R homologue amino acid sequences (PDF 187 KB)
11262_2018_1613_MOESM13_ESM.pdf (223 kb)
Multiple sequence alignment of Kelch like protein gene sequences (PDF 223 KB)
11262_2018_1613_MOESM14_ESM.pdf (171 kb)
Multiple sequence alignment of Kelch like protein amino acid sequences (PDF 170 KB)
11262_2018_1613_MOESM15_ESM.pdf (8 kb)
Phylogenetic analysis of Capripoxviruses using Mega 6.0 using GPCR sequences. Phylogeny was constructed using Tamura 3 parameter + G model in Maximum likelihood method. The bootstrap values at each node or sub node indicate the reliability classifying the Capripoxviruses into distinct classes (PDF 8 KB)
11262_2018_1613_MOESM16_ESM.tif (2.1 mb)
Phylogenetic analysis of Capripoxviruses using Mega 6.0, with whole genome sequences (TIF 2156 KB)
11262_2018_1613_MOESM17_ESM.docx (17 kb)
Supplementary material 17 (DOCX 17 KB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Bina Mishra
    • 1
    Email author
  • Piyali Mondal
    • 2
  • C. L. Patel
    • 1
  • Insha Zafir
    • 1
  • Rachna Gangwar
    • 1
  • Neha Singh
    • 2
  • Joyshikh Sonowal
    • 2
  • Deepanker Bisht
    • 2
  • Amit Ranjan Sahu
    • 2
  • Mumtaz Baig
    • 3
  • Basavaraj Sajjanar
    • 2
  • R. K. Singh
    • 2
  • Ravi Kumar Gandham
    • 2
    • 4
  1. 1.Division of Biological ProductsICAR-Indian Veterinary Research InstituteBareillyIndia
  2. 2.Division of Veterinary BiotechnologyICAR-Indian Veterinary Research InstituteBareillyIndia
  3. 3.Department of Zoology, Laboratory of Molecular and Conservation Genetics (LMCG)Govt. Vidarbha Institute of Science & HumanitiesAmravatiIndia
  4. 4.National Institute of Animal Biotechnology (NIAB)HyderabadIndia

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